cher-class(Ringo)
cher-class()所属R语言包：Ringo
Class "cher" - ChIP-enriched region
类“雪儿” - 芯片富集区域
译者：生物统计家园网 机器人LoveR
描述----------Description----------
An object of class cher (ChIP-enriched region) holds characteristics of an enriched genomic region from ChIP chip
类cher（芯片丰富的区域）的对象拥有丰富的基因组区域的特点，从芯片芯片
类的对象----------Objects from the Class----------
Objects can be created by calls of the form new("cher", name, chromosome, start, end, cellType, antibody, maxLevel, score, probes, extras, ...).
创建对象可以通过检测的形式new("cher", name, chromosome, start, end, cellType, antibody, maxLevel, score, probes, extras, ...)。
插槽----------Slots----------
name: character vector of length 1 unequivocally
name：明确的长度为1的字符向量
chromosome: character vector of length one, naming the
chromosome：字符长度为1的向量，命名
start: integer, region start position on the
start：integer，区域上的起始位置
end: integer, region end position on the
end：integer，区域的结束位置
cellType: character vector describing the cell type the ChIP chip experiment has been done on,
cellType：character矢量描述的单元类型的芯片芯片实验已经做了，
antibody: character vector describing the antibody or characteristic for which fragments were supposedly enriched in immuno-precipitation step,
antibody：character矢量描述的抗体或片段据说在免疫沉淀步骤丰富的特点，
maxLevel: numeric, maximal (smoothed) probe
maxLevel：numeric，最大（平滑）探针
score: numeric of a cher score, currently we use the sum of smoothed probe levels (log fold changes),
score：numeric的雪儿得分，目前我们使用的平滑探测器水平的总和（登录倍的变化），
probes: vector of probe identifiers
probes：vector探针标识
extras: list of further elements used to annotate the cher; examples of such that are used in Ringo are:
extras：list用来注释的cher进一步元素中所使用的例子，如Ringo是：
typeUpstream optional character vector of features that this cher is located upstream of, e.g. the transcriptional start site of "ENST00000379158".
typeUpstream可选特征的特征向量，这cher位于上游，例如：转录起始位点“ENST00000379158”。
typeInside optional character vector of features
typeInside可选字符向量功能
distMid2TSS optional named numeric vector of distances of the cher's middle position to features, e.g. TSSs of features upstream and inside; names are the features to which the distances are given; only meaningful in combination with typeUpstream and
distMid2TSS可选的命名数值cher的中间位置的距离矢量的功能，例如：上游和内部功能的起始位置跟名称是距离给定的功能，只有结合有意义的typeUpstream
upSymbol optional character vector of gene symbols of features the cher is located upstream of; supplements
upSymbol可选功能雪儿的基因符号特征向量位于上游;补充
inSymbol optional character vector of gene symbols of features the cher is located upstream of; supplements
inSymbol可选功能雪儿的基因符号特征向量位于上游;补充
... further list elements can be added using the
...进一步的列表元素可以添加使用
方法----------Methods----------
initialize create a new cher; see section
初始化创建一个新的cher;参见
plot calls chipAlongChrom to plot the
图调用chipAlongChrom绘制
update signature(cher,...); updates elements of the cher object; The further arguments in '...' are interpreted. Arguments corresponding to defined slot names of the cher result in the value by that slot being replaced by the specified value for the argument; argument names that do not correspond to slot names of the object result in list elements of the extras list of the cher being replaced by the given values for these arguments or the values are appended to the current extras list and the argument names make up the list names of the appended arguments. See section
更新的签名（cher，...）;更新cher对象的元素，在进一步的论据“......解释。参数对应的插槽名称;cher结果在该插槽被替换为参数指定值的值定义的参数名称不符合对象的结果列表元素<插槽名称X>列表extras被替换这些参数值的给定值追加到当前cher列表和参数名的附加参数列表名称。见第
cellType obtain or replace the description of the cell type,
cellType获取或更换的单元类型的描述，
probes obtain the vector of probes involved in a
探针得到探针的向量中涉及
cherList----------cherList----------
A list in which each element is of class cher, is called a cherList. This class, however, is rarely used (yet).
一个列表，其中每个元素是类cher，被称为cherList。然而，这个类，很少使用（还）。
注意----------Note----------
The cher class used to be an S3 list before.
cher类是S3名单之前。
The term 'cher' is shorthand for 'ChIP-enriched region'. We think this term is more appropriate than the term 'peak' commonly used in ChIP-chip context. Within such regions the actual signal could show two or more actual signal peaks or none at all (long plateau).
“雪儿”是芯片富集区域“的缩写。我们认为这个词是较适宜在芯片芯片的情况下常用的“高峰”。在这些区域的实际信号可以显示实际信号的两个或两个以上的山峰或根本没有（术语高原）。
作者（S）----------Author(s)----------
Joern Toedling, Tammo Krueger
参见----------See Also----------
plot.cher, findChersOnSmoothed, relateChers
plot.cher，findChersOnSmoothed，relateChers
举例----------Examples----------
## how to create a cher object from scratch[＃如何从头开始创建雪儿对象]
cherNudt2 <- new("cher", name="nudt2.cher", chromosome=9,
start=34318954, end=34319944, antibody="Suz12",
maxLevel=2.00, score=69.2, upSymbol="NUDT2")
#extras=list(upSymbol="NUDT2"))[演员=列表因素（upSymbol =的“NUDT2”））]
cherNudt2
str(cherNudt2)
## use the update method (note:this update is biologically meaningless)[＃使用更新的方法（注：此更新是生物意义）]
cher2 <- update(cherNudt2, cellType="HeLa", downSymbol="P53",
probes=c("probe1","probe2"))
cher2; str(cher2)
## plot a cher object[＃绘制雪儿对象。]
exDir <- system.file("exData",package="Ringo")
load(file.path(exDir,"exampleProbeAnno.rda"))
load(file.path(exDir,"exampleX.rda"))
smoothX <- computeRunningMedians(exampleX, probeAnno=exProbeAnno,
modColumn = "Cy5", allChr = "9", winHalfSize = 400)
plot(cherNudt2, smoothX, probeAnno=exProbeAnno, gff=exGFF, extent=5000)
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-2-26 12:56:29
